5YFP

Cryo-EM Structure of the Exocyst Complex

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.025
f_angle_d	1.331
f_chiral_restr	0.056
f_bond_d	0.006
f_plane_restr	0.006

Sample
Cryo-EM map of the Yeast Exocyst complex overall structure at 5.5A resolution
Sample Components
Cryo-EM map of the yeast Exocyst complex head-part structure at 6.7A resolution
Cryo-EM map of the yeast Exocyst complex top head-part structure at 6.2A resolution
Cryo-EM map of the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
Cryo-EM map of the yeast Exocyst complex body-part structure at 4.4A resolution
Cryo-EM map mask for the Yeast Exocyst complex overall structure at 5.5A resolution
Cryo-EM map mask for the Yeast Exocyst complex head structure at 6.7A resolution
Cryo-EM map mask for the yeast Exocyst complex top head-part structure at 6.2A resolution
Cryo-EM map mask for the yeast Exocyst complex bottom leg-part structure at 4.6A resolution
Cryo-EM map mask for the yeast Exocyst complex body-part structure at 4.4A resolution

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Protein sample was applied onto a Quantifoil R1.2/1.3 golden grid and hold for 60 seconds, then blot for 2.5 seconds before plunging.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	343342
Reported Resolution (Å)	4.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	Refinement Space	Refinement Protocol	Refinement Target	Overall B Value	Fitting Procedure	Details
1 (2B1E)	REAL	RIGID BODY FIT				Exo70 (a.a.67-623) was first fit into the map with Situs as a rigid body. Then it was split as Exo70 (a.a.67-344) and Exo70 (a.a.345-623), and fit into the same position with Chimera.
2 (2D2S)	REAL	RIGID BODY FIT				Well fit by one step Situs fitting.
3 (2FJI)	REAL	RIGID BODY FIT				The fitting position of this chain was determined by cross-link mass spectrum.
4 (5H11)	REAL	RIGID BODY FIT				The yeast Sec10 (a.a.234-867) model was first obtained with Swiss-Model prediction based on this zebrafish originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
5 (1ZC4)	REAL	RIGID BODY FIT				The yeast Exo84 (a.a.346-470) model was first obtained with PHYRE2 prediction based on this rat originated initial model, and then fit into the map. Final refinement was proceeded with Phenix real-space refinement.
6 (2A2F)	REAL	RIGID BODY FIT				The yeast Sec15 (a.a.482-896) model was first obtained with PHYRE2 prediction based on this Drosophila originated initial model, and then fit into the map. Local adjustment was made with Coot. Final refinement was proceeded with Phenix real-space refinement.
7 ()	REAL	BACKBONE TRACE				All remaining models were manually built as backbone tracing Poly-Alanine, yet the present residues are shown as original. The backbone trace was guided by the EM map connectivity, secondary structure prediction and cross-link mass spectrum. The model was validated with different sets of cross-link mass spectrum data to confirmed the correctness.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	2000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	22500
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	1.4
IMAGE ACQUISITION	UCSFImage	4
CTF CORRECTION	RELION	1.4
MODEL FITTING	Situs	2.8
MODEL FITTING	Chimera	1.10.1
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Situs	2.8
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Chimera	1.10.1
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Chimera	1.10.1
MODEL REFINEMENT	Coot	0.8.2
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Chimera	1.10.1
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Chimera	1.10.1
MODEL REFINEMENT	Coot	0.8.2
MODEL REFINEMENT	PHENIX	1.11.1
MODEL FITTING	Coot	0.8.2
MODEL REFINEMENT	PHENIX	1.11.1
INITIAL EULER ASSIGNMENT	RELION	1.4
FINAL EULER ASSIGNMENT	RELION	1.4
CLASSIFICATION	RELION	1.4
RECONSTRUCTION	RELION	1.4

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	The defocus value of each image was determined by CTFFIND3.	904481	Semi-auto-picked by RELION1.4.